Using a GL-5 in a manual trans indeed won't hurt it but...it won't help it either.
GL-5 is a specification for gear oils used to lubricate hypoid rear axle gear sets. Because the teeth in hypoid gears slide across each other as well as mesh, a GL-5 needs a lot of extreme pressure additives to make the lubricant effective.
There is the description of GL-5 according to API's web site.
API Category GL-5 designates the type of service characteristic of gears, particularly hypoids in automotive axles under high-speed and/or low-speed, high-torque conditions. Lubricants qualified under U.S. Military specification MIL-L-2105D (formerly MIL-L-2015C), MIL-PRF-2105E and SAE J2360 satisfy the requirements of the API GL-5 service designation.
GL-4 is a specification for gear oils used to lubricate light duty rear axle gear sets along with helical and straight cut gears in transmissions. Here is the descrption of GL-4 according to API's site
API Category GL-4 designates the type of service characteristic of spiral-bevel and hypoid gears in automotive axles operated under moderate speeds and loads. These oils may be used in selected manual transmission and transaxle applications.
As a result, a GL-4 doesn't require as much EP additives and that is a good thing because the amount of EP additives in GL-5 gear oils can actually degrade synchronizer action. Cone synchos, used in Muncies, and many other manual transmssions, depend on a certain level of friction for proper synthronizer action. If that level of friction is not available because of the EP addtives in a GL-5, shift feel is compromised. Sometimes the driver's reaction is to just push harder on the shfiter and occasionally that results the transmission grinding. in the long-term, you risk decreased durability of the sychronizers with a GL-5 gear lube whereas with a GL-4 you do not.
Exxon-Mobil comes right out on its web site and says it does not recommend use of GL-5 lubricants in manual transmissions. There are other lubricant makers which state the same.
While some GL-5s are labeled "multi-purpose" and said by their markers to be good for use in manuals with cone-type synchros, but the best choice is always a GL-4. You'll get the best shift feel and the best synthronizer life.
For more info do Google search with keywords GL-4 SAE90 gear oil.